Commander Cain had the brilliant idea of jumping to lightspeed at the exact moment the battlestar he was alongside exploded. The Cylons thought that BOTH of them were destroyed casue of the proximity (and if Cain hadn't jumped , more than likely that's exactlywhat would have happened , or if their calculations were off.)
After that he did hit and run warfare going deeper into cylon territory so any Colonial remnants (like Galactica) can run far and fast with less pursiut as the Cylons started payingmore attention to their backyard. Eventually he realises it's getting too dangerous as the Cylons close their net on the Pegasus so he bails out of the Cylon territories and ends up finding Galactica by following the cylons reinforcing the forward pursiut forces.
When last we see him and the Pegasus they throw off Galactica's pursuers by engaging two Base Stars at point blank range and firing all their nukes broadside totally destroying the Cylons. It is assumed they died in the explosionand the return fire of the Cylons.
It was Adama's belief that Cain simply used this as an opportunity to disappear again lie before and is even now harrasing the Cylons behind their lines...
